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0012801

Visomics

[All Projects] General

public

2012-01-06 15:43

Reporter

Brian Helba

Assigned To

Priority

low

Severity

minor

Reproducibility

have not tried

Status

new

Resolution

open

Platform

Ubnutu Linux

OS Version

Summary

0012801: R package installation on user-built Linux R

Description

When using the 'make RExternalPackages' target, JC is unable to install the 'preprocessCore' package on his machine (Ubuntu Linux with a user-built copy of R in the home directory, not installed).

The 'pls' package installs fine, and the 'preprocessCore' package installs correctly when tried directly from the R command line using:
source("http://www.bioconductor.org/biocLite.R" [^])
biocLite("preprocessCore")

Once the package is installed, the Make target is able to correctly verify the fact.

Additional Information

Checking for R package 'pls'...
  Package 'pls' not found installing...
trying URL 'http://cran.r-project.org/src/contrib/pls_2.1-0.tar.gz' [^]
Content type 'application/x-gzip' length 228265 bytes (222 Kb)
opened URL
==================================================
downloaded 222 Kb

* installing *source* package ‘pls’ ...
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (pls)

The downloaded packages are in
    ‘/tmp/Rtmp8LElZM/downloaded_packages’
Updating HTML index of packages in '.Library'
Checking for R package 'preprocessCore'...
  Package 'preprocessCore' not found installing...
BioC_mirror = http://www.bioconductor.org [^]
Change using chooseBioCmirror().
Using R version 2.11.1, biocinstall version 2.6.10.
Installing Bioconductor version 2.6 packages:
[1] "preprocessCore"
Please wait...

trying URL 'http://www.bioconductor.org/packages/2.6/bioc/src/contrib/preprocessCore_1.10.0.tar.gz' [^]
Content type 'application/x-gzip' length 116631 bytes (113 Kb)
opened URL
==================================================
downloaded 113 Kb

* installing *source* package ‘preprocessCore’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for pthread_create in -lpthread... yes
checking if we can use pthreads... yes
checking if PTHREAD_STACK_MIN is defined... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
make[3]: *** read jobs pipe: No such file or directory. Stop.
make[3]: *** Waiting for unfinished jobs....
ERROR: compilation failed for package ‘preprocessCore’
* removing ‘/home/jchris/Projects/Bioinformatics/R-2.11.1/library/preprocessCore’

The downloaded packages are in
    ‘/tmp/Rtmp8LElZM/downloaded_packages’
Updating HTML index of packages in '.Library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, ...) :
  installation of package 'preprocessCore' had non-zero exit status

Issue History
Date Modified	Username	Field	Change
2012-01-06 15:43	Matthew Bowman	New Issue

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